Diego Simeone's side have often struggled in this part of Andalusia and so that proved again on Sunday, despite Angel Correa's 18th-minute opener.
Atleti would have been two in front if not for Geoffrey Kondogbia, who got a touch to Marcos Llorente's goal-bound effort for the strike to be ruled out for offside.
El Bilal Toure headed in soon after and Almeria saw out a draw that leaves fourth-placed Atleti, who had Sergio Reguilon sent off late on, 13 points adrift of leaders Barcelona.
Atleti took the lead after Antoine Griezmann dummied Kondogbia's pass for Correa to collect and tuck through the legs of Fernando Martinez.
Llorente's shot 14 minutes later appeared to be heading for the net without the need for any intervention, but Kondogbia turned it in from an offside position.
Kondogbia's misjudgement proved costly in the 37th minute when Toure powered a diving header past Jan Oblak after meeting Lucas Robertone's right-sided cross.
Correa and Alvaro Morata should have done better with efforts that were kept out by Martinez, with the latter also heading wide from a glorious position.
Atleti substitute Reguilon was sent off in the closing stages after receiving two yellow cards in the space of four minutes, as Atleti's disappointing run of form stretched to just one win in six league matches.